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Protein Structure Prediction

Image credit: FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours

Papers

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Showing 101–150 of 188 papers

TitleStatusHype
Recent advances in interpretable machine learning using structure-based protein representations—0
Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion—0
Seq-SetNet: Exploring Sequence Sets for Inferring Structures—0
SGNet: Folding Symmetrical Protein Complex with Deep Learning—0
Simultaneous identification of specifically interacting paralogs and inter-protein contacts by Direct-Coupling Analysis—0
Sparse, guided feature connections in an Abstract Deep Network—0
Structural Property Prediction—0
Structure Alignment—0
Structure determination—0
Technical Report of HelixFold3 for Biomolecular Structure Prediction—0
tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modeling Structure Refinement—0
The curious case of A31P, a topology-switching mutant of the Repressor of Primer protein : A molecular dynamics study of its folding and misfolding—0
The prospects of quantum computing in computational molecular biology—0
Thermodynamics of Protein Folding—0
TOPO: Improving remote homologue recognition via identifying common protein structure framework—0
Transformers in Protein: A Survey—0
Understanding Biology in the Age of Artificial Intelligence—0
Unfolding AlphaFold's Bayesian Roots in Probability Kinematics—0
Variational Inference for Sparse and Undirected Models—0
"Weak AI" is Likely to Never Become "Strong AI", So What is its Greatest Value for us?—0
Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data—0
What is an equivariant neural network?—0
3D RNA and functional interactions from evolutionary couplings—0
AlphaFolding: 4D Diffusion for Dynamic Protein Structure Prediction with Reference and Motion Guidance—0
6DCNN with roto-translational convolution filters for volumetric data processing—0
A Comprehensive Review of Generative AI in Healthcare—0
Advanced Deep Learning Methods for Protein Structure Prediction and Design—0
Advances of Deep Learning in Protein Science: A Comprehensive Survey—0
A Hybrid Local Search for Simplified Protein Structure Prediction—0
A Hybrid Monte Carlo Ant Colony Optimization Approach for Protein Structure Prediction in the HP Model—0
AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification—0
AI in Pharma for Personalized Sequential Decision-Making: Methods, Applications and Opportunities—0
AIS-INMACA: A Novel Integrated MACA Based Clonal Classifier for Protein Coding and Promoter Region Prediction—0
Aligning Protein Conformation Ensemble Generation with Physical Feedback—0
AlphaCrystal-II: Distance matrix based crystal structure prediction using deep learning—0
AlphaFold2 for protein structure prediction: Best practices and critical analyses—0
A Model-Centric Review of Deep Learning for Protein Design—0
AmoebaContact and GDFold: a new pipeline for rapid prediction of protein structures—0
An Automated Global Method for Extraction of Distance Distributions from Electron Spin Resonance Pulsed Dipolar Signals—0
A new hybrid genetic algorithm for protein structure prediction on the 2D triangular lattice—0
An Investigation in Optimal Encoding of Protein Primary Sequence for Structure Prediction by Artificial Neural Networks—0
Applications of Knot Theory for the Improvement of the AlphaFold Protein Database—0
A Protein Structure Prediction Approach Leveraging Transformer and CNN Integration—0
Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models—0
A Survey of Deep Learning Methods in Protein Bioinformatics and its Impact on Protein Design—0
AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy—0
Beating the Best: Improving on AlphaFold2 at Protein Structure Prediction—0
Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation—0
Beyond Current Boundaries: Integrating Deep Learning and AlphaFold for Enhanced Protein Structure Prediction from Low-Resolution Cryo-EM Maps—0
Capturing the geometry, function, and evolution of enzymes with 3D templates—0
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All datasetsCASPSeqCASPSimSeqPaenSeqUniProtSeq

Benchmark Results

#ModelMetricClaimedVerifiedStatus
1GAL 125MValidation perplexity20.62—Unverified
2GAL 1.3BValidation perplexity17.58—Unverified
3GAL 6.7BValidation perplexity17.29—Unverified
4GAL 30BValidation perplexity17.27—Unverified
5GAL 120BValidation perplexity17.26—Unverified
#ModelMetricClaimedVerifiedStatus
1GAL 125MValidation perplexity19.18—Unverified
2GAL 1.3BValidation perplexity17.04—Unverified
3GAL 6.7BValidation perplexity16.35—Unverified
4GAL 30BValidation perplexity15.42—Unverified
5GAL 120BValidation perplexity12.77—Unverified
#ModelMetricClaimedVerifiedStatus
1GAL 125MValidation perplexity16.35—Unverified
2GAL 1.3BValidation perplexity12.53—Unverified
3GAL 6.7BValidation perplexity7.76—Unverified
4GAL 30BValidation perplexity4.28—Unverified
5GAL 120BValidation perplexity3.14—Unverified
#ModelMetricClaimedVerifiedStatus
1GAL 125MValidation perplexity19.05—Unverified
2GAL 1.3BValidation perplexity15.82—Unverified
3GAL 6.7BValidation perplexity11.58—Unverified
4GAL 30BValidation perplexity8.23—Unverified
5GAL 120BValidation perplexity5.54—Unverified